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The Malhi Molecular Anthropology and Ancient DNA Labs

I’ve known Ripan Malhi for years now, but until this past week, I had never met him in person. Dr. Malhi attempted to extract the DNA from both a stamp, supposedly licked by my grandfather, and my father’s hair, complete with follicle. I could hardly wait those long days to determine if any DNA was present. I tried not to pester him, but I felt like the proverbial child constantly asking “are we there yet?”

Unfortunately, none of the multiple attempts were successful, but they established a relationship between Ripan and myself. Ripan and I were trying to figure out this week just how long ago that was and we think it was about 10 years. We know it was more than 7 years, since he has been at the University of Illinois since 2006 where he established the Malhi Labs, and it was significantly prior to that.

After finishing his PhD, Ripan founded a company called Trace Genetics. It was there that I first met Ripan. They specialized in ancient DNA processing. A few years later, in 2006, Ripan sold that company and established both the Malhi Ancient DNA Lab and the Malhi Molecular Anthropology Lab at the University of Illinois where he is an Associate Professor.

Ripan has a long list of publications to his credit. It won’t surprise you to discover that Native American and ancient DNA are both areas in which he specializes, and in particular, ancient Native American DNA.

The Malhi Molecular Anthropology Laboratory generates DNA variation data from different genetic systems (i.e. mitochondrial genome, Y chromosome, autosomal) to infer evolutionary history of populations and species. Currently, research in the lab is split into two independent research areas, the evolutionary history of Native Americans and evolutionary genetics of non-human primates in the areas of:

Molecular Anthropology

Ancient DNA Analysis

Evolutionary Genomics

Forensic Science

Population Genetics

Dr. Malhi was very gracious during my visit to the University of Illinois and agreed to show me both of his labs. Not only that, he came to the Native American House to get me so that I wouldn’t get lost navigating the campus and delivered me back as well. For that, I’m extremely grateful! A campus with 40,000 students isn’t a campus, it’s a city and parking is almost non-existent!

First we visited the Ancient DNA Lab. This lab is separate from the rest of the processing, and is actually in a different building altogether. Access is extremely limited and only those who need to go inside, do. I’m not one of those people.

Why such limited access? In a word, contamination, the arch-nemesis of ancient DNA processing. Ancient DNA, by definition is old, degraded and generally in short supply. The process of extracting it from whatever medium you are working with, teasing out whatever is left, without introducing any outside contamination, is tricky at best. Limiting the exposure in the room itself is the first step in a series of protocols designed to limit, prevent and then identify contamination if it exists.

The room is double air locked and pressurized so that when someone enters or exists the air is blown out and none of the surrounding air enters the lab.

The room itself can accommodate two researchers. The window is tinted yellow as the lighting is also controlled within the lab. So if these photos look yellow, it’s because they are.

You can see the DNA extraction area in this photo. Work is done inside a cubicle, again, to limit contamination. You can see the mortar and pestle used to sometimes grind the materials. Other times, such as with teeth, drills are used.

After the DNA is extracted and amplified, assuming DNA is found, and it’s not contaminated, the results are then taken to the second lab, down the street, for processing.

This is the Molecular Anthropology lab where most of the people work, since they deal only with already extracted ancient DNA or contemporary DNA.

Contemporary DNA is considered a medical hazard while the DNA is still in a body fluid of some type (saliva, blood, cheek swab), so medical precautions must be taken. In many ways, this lab looks just like a lab at a medical facility. In fact, it’s in the Medical Sciences building.

DNA is extracted from contemporary samples in this work area. After extraction, it is no longer considered a medical hazard, so from that point forward, only normal lab protocols are in force, not medical biohazard protection.

The DNA is then further processed in this area. Ripan discussed some of his current projects as we toured. He continues his work on Native American population genetics, and in particular, the migration and settlement of the Native people on this continent. Currently he collaborates with Canadian tribes and is involved with an ongoing project to analyze the remains of several hundred Native burials that have previously been discovered.

Not only does he work with Native population genetics, and remains, but he also encourages Native American students to join his programs and work in the labs. He works closely with the Native American House.

I’m hopeful that Ripan’s projects and ongoing analysis will bring some answers to questions like whether or not mitochondrial haplogroup X is found in any tribes west of the St. Lawrence Seaway (inferring that it did come from Asian, not Europe), whether haplogroup M is found in the founding Native population and whether European or African haplogroups of any description are found pre-Columbian contact in the Americas.

I want to thank Dr. Malhi for his hospitality, for making time for the tour this week, and to wish him Godspeed in his continuing research. And yes, that does mean I want him to hurry. That hasn’t changed in the past decade!

Thanks, Roberta, for this very interesting article-I hope you are ok with me sharing. A question: There are some Hayes relatives that have been told by our ancestors that William Jasper Hayes (my maternal grandfather) is one-half Indian-I have not seen any documentation that would establish this – however, learning about Dr. Malhi’s work opens some new possibilities in our search for William Jasper’s parents. He died in 1930 and is buried in Northeast Oklahoma. What would be the logical procedures to have his DNA tested? I would appreciate your thoughts. Thanks, B. Horn

You could test yourself using the Family Finder ethnicity test. If this is your grandfather and he was half Indian, you should be approximately 12.5% Native. Secondly, you could test one of his sons or other males who carry the surname. Third, if he had sisters, you could check the mtdna of someone who descends from the sisters through all females.

Greetings!!
I am an Indian student and currently working on an Ancient DNA project. My samples contain degraded DNA, i tried extracting Ancient DNA but not 100% successful. I would like to know whether you can help me anyway in analyzing my samples.
Thanks,
Sonal.

Roberta, this is a very interesting article. His field of studying Native American DNA is fascinating, and it would be nice getting periodical updates on his research! I am hoping that major strides are made on ancient DNA.